The away team explains to Conor and Martin Benbeck that given the nature of the stellar core fragment evacuation may be inevitable. However, Conor and Benbeck explain that it is in fact imperative that they remain on the planet and preserve the colony. It is explained to Commander Riker, CounselorTroi and Lieutenant CommanderLa Forge that this is a genetically-engineered society; their ancestors came from Earth to create a perfect society, believing that through controlled procreation they could create people without flaws and those people would build a paradise. They have evolved beyond Humanity. They also explain that they have achieved a fully integrated existence with their environment, thanks also to their master design. They cannot separate themselves from it without irreparably altering who and what they are.

Benbeck, who is the interpreter of the colony founders' wishes, is the one who continually emphasizes the importance of preserving the balance of their society. He dislikes the away team's presence. Conor, on the other hand, is more receptive: he understands the necessity of them being here, and being the diplomat he is, welcomes them, and allows La Forge to work with Hannah Bates – their top astrophysicist – to find a solution. He even begins to find a liking in counselor Troi. However, he reiterates that this is a perfect existence for them which they will not give up easily.

When Bates shows La Forge a design for a multiphasic tractor beam, he believes the Enterprise could use it to move the fragment just enough to reduce the effects below dangerous levels. However, he would need her assistance in setting it up, which means she would have to leave the colony and beam up to the Enterprise.

Benbeck strongly objects, arguing that her absence would create a dangerous imbalance. Insistent though he is, Conor overrules him, and she is beamed aboard.

"Captain's log, supplemental. Commander La Forge and Hannah Bates have spent three days trying to find a way to adjust the path of the core fragment. If they do not succeed in the next 48 hours, we will need to begin evacuation."

While discussing the matter with CaptainPicard, Troi notes that some of the colonists would chose to risk death rather than leave. Picard, who is opposed to the very idea of genetic engineering, has a hard time buying that. He thinks it is a bad idea whose time has long passed. In his opinion, the genetic engineering practiced by the founders of the colony eliminates much of the qualities that make life worth living. He advises Troi to use Conor's openness to suggestions and reasonable attitude, as well as her personal admiration for him, to help him see the reality of the situation and convince others to do the same.

Meanwhile, as Bates and La Forge work on their multiphasic tractor beam, they find that it would overload some of the power conduits. As they try to come up with a solution, a tired La Forge takes his VISOR off, and she sees his non-functioning eyes. He bitterly observes that he probably wouldn't be here, were he born on their world, likely terminated as a fertilized cell. When she asks about how it works, he explains it to her and suddenly has an idea as how to solve the problem: he suggests using the same technology that his VISOR utilizes. He chuckles, saying that it would be an irony if the answer to all of this is in a device created for a blind man who never would have existed in their society.

Down on the planet, during a piano recital by Matthew, there is an earthquake. It is the first tremor of what would become many. Counselor Troi is strongly attracted to Conor, almost falling in love. That's when she realizes that this is all wrong. Conor is obviously changed, ever since the Enterprise has been in touch with the colony, and she is concerned that this is affecting his decision making. He seems willing to throw everything away for her, not just for the survival of the colony. While they are discussing the situation, La Forge and Bates beam down on the planet stating that a team of fifty engineers from the Enterprise is needed to reinforce the structure and solve their problem. Conor agrees.

"Captain's log, supplemental. The Enterprise has moved to a parallel course with core fragment. We must adjust its trajectory by a minimum of 1.2 degrees to ensure the colony's safety."

Bates and La Forge activate the tractor beam in engineering and begin to use it on the fragment. Slowly but surely, the Enterprise pushes the fragment away, almost losing life support in the process. Conor is pleased, as is everyone on the colony. He is patched through to Bates and tells her the entire colony will celebrate her return. After the channel is closed, Bates walks away, looking reluctant to returning.

"Captain's log, supplemental. The stellar core fragment has passed safely out of the Moab system. The colony was shaken by powerful tremors, but fortunately there were no injuries, and only minor damage was reported."

It is only now, after most of the engineering crews have left, that the damage has been done. When Bates indicates a breach in the artificial biosphere and goes to the lab to analyze it, La Forge points out that there is no such breach for his VISOR's positronic scan would have detected even the smallest crack. He concludes she faked the incidence. Bates admits she did that because of her encounters outside her world: if she's so brilliant, she wonders, why didn't she invent starships or deflector shielding. As a result, she requests asylum, and Riker indicates she may not be the only one wishing to leave.

Captain Picard himself finally takes this opportunity to meet Aaron Conor. Benbeck immediately starts attacking Picard, saying all of these people wanting to leave is his fault. Conor decides to talk to Captain Picard alone, and explains he didn't want to listen to Martin from the first moment they were hailed. He understands the desire to leave, with a curiosity about the outside world, and feels responsible for it happening. He asks that Picard refuse them passage, since his leaving will solve the problem he created with his arrival. Picard points out that this is simplistic. He cannot deny their human rights, whatever other consequences it may have. However, he is willing to try to dissuade them from leaving. Unfortunately, they fail to persuade the people to stay.

The Enterprise takes them, 23 in all, as Conor wonders about what his mistake was. And Picard points out this is the best reminder of the Prime Directive, but Riker reminds Picard that because they're Human, the Prime Directive does not apply. Despite that technicality, Picard realizes they may have been just as destructive as any core fragment could ever have been.

"Oh, that's perfect."
"What?"
"If the answer to all of this is in a VISOR created for a blind man who never would have existed in your society."

- La Forge and Hannah Bates

"My VISOR's positronic scan would have detected the leak. Its molecular-pattern enhancer would pick up even the smallest crack."
"The damn thing doesn't miss much, does it?"

- La Forge and Hannah Bates

"They've managed to turn a dubious scientific endeavor into dogma."

- Picard

"They've given away their Humanity with this genetic manipulation. Many of the qualities that they breed out – the uncertainty, self-discovery, the unknown – these are many of the qualities that make life worth living. Well, at least to me. I wouldn't want to live my life knowing that my future was written, that my boundaries had been already set."

"We are responsible."
"We had to respond to the threat of the core fragment, didn't we?"
"Of course we did. But, in the end... we may have proved just as dangerous to that colony as any core fragment could ever have been."

- Picard and Riker discussing the fate of the now crippled Genome colony (last lines)

David Livingston recalled that visualizing the biosphere proved to be a challenging task for the production team. "Rick wanted to make sure we could see the effects outside the window. He didn't want to do what we normally do on stage, which was something tangible and real. That presented some challenges to the director, because the blue screen was right in the middle of the set, but he shot around it a little bit and I think it worked out successfully." (Captains' Logs: The Unauthorized Complete Trek Voyages)

Regarding this episode's clear focus upon themes of eugenics and genetic engineering, Picard refers to them as a "dubious scientific endeavor" whose "time has passed", which perhaps mirror humanity's experience through the Eugenics Wars or Khan, although no direct mention is done. Earlier in the season, he explicitly refers to Khan as a tyrant, comparing him to Adolf Hitler in "A Matter of Time". Eugenics have also been featured in "Unnatural Selection" although there was no overt criticism from Picard. His disapproval was, however, implied when he responds to the genetically-engineered humans being referred to as the future of humanity with "At least Doctor Kingsley's vision of it."

Piller remarked, "This was the beginning of me feeling better about the season. It was another one of these shows that had been around for awhile and a lot of writers had taken a shot at. It dealt with genetic engineering and abortions and interesting things for Geordi to do, and the relationship between Troi and the leader of the society. I think it's a real classic tragedy, because everybody was trying to do the right thing in that episode and it ended up in destruction. Aside from some disappointment in casting, I was rather pleased with that. I think a lot of people were rather pleased they liked it as much as they did." (Captains' Logs: The Unauthorized Complete Trek Voyages)

Other members of the production staff were not as enthused by the final episode. Rick Berman stated, "It's a very philosophical issue that we felt seriously about, and a show that I thought was disappointing and didn't turn out as well as I had hoped. It was slow and talky and we had casting problems. As for the abortion issue, that's nonsense. It was totally unintended. I think that there are very few people on our writing staff who would be involved with something that would be a non-choice outlook." (Captains' Logs: The Unauthorized Complete Trek Voyages)

Ronald D. Moore remarked, "This is another example of a show that doesn't really work too well. We sort of show up at a genetically perfect colony – which in and of itself is starting to bore me – and when we get there, it's 'Gee, Troi falls in love with one of the people.' You can't wait to get up and get a beer." (Captains' Logs: The Unauthorized Complete Trek Voyages)

Director Kolbe also remarks, "I liked that idea, but I'm not satisfied with the casting. I don't think the episode had enough energy. Maybe it's unfair to blame the casting. Maybe I just didn't give it the energy. I liked the concept and the script. I just didn't like the show." (The Official Star Trek: The Next Generation Magazine Vol. 21, p. 31)